More options

There are more options that influence the quality of the alignment (minimum length, percent identity) or change the output format and reported quantities (NCBI taxID, full rank, summarizing at a specific taxonomic rank). These options are displayed when
using the plain $motus profile command:

$motus profile

2. Generating metatranscriptomic profiles

Standard example

Metatranscriptomic profiles can be generated using the profile command and one or more sequencing files in fastq format:

More options

There are more options that influence the quality of the alignment (minimum length, percent identity) or change the output format and reported quantities (NCBI taxID, full rank, summarizing at a specific taxonomic rank). These options are displayed when
using the plain $motus profile command:

$motus profile

3. Generating single nucleotide variant (SNV) profiles using MGs

Calling variants using marker genes is divided in to two subroutines, namely alignment and variant calling (map_snv, snv_call). map_snv aligns sequencing reads against the mOTU profiler database. snv_call utilizes
the metaSNV package to call variants on these marker genes.

map_snv takes one or multiple sequencing files and aligns reads against the mOTU profiler database:

snv_call takes the bam files created in the map_snv step as input and calls variants using the metaSNV package. This information is then be used to create a distance matrix between samples. The input for snv_call is a directory with bam files. Each bam
file will be treated as an individual sample:

motus snv_call -d DIRECTORY -o OUTPUT_DIRECTORY

An example distance matrix for the comparison of 3 samples is shown below.

There are multiple filtering parameters that influence if variants are called such as coverage depth (-fd), coverage breadth (-fb) or the minimum number of samples that report a variant (-fm). A list of all parameter can be found when executing the plain
motus snv_call command: